In agro-based economies with limited industrial resources, such as Paraguay, there is a pressing need for accessible tools that support the sustainable management and optimization of agro-industrial byproducts. This study presents Life Cycle Assessment (LCA) as a decision-making and optimization tool for industrial processes, applied to the valorization of Acrocomia aculeata endocarp—an abundant yet underutilized byproduct from the palm fruit industry that is widely processed in Paraguay. This work provides an LCA estimate that defines system boundaries and includes transport and potential packaging scenarios. The LCA covers the pathway from waste generation (endocarp produced during processing) through its conversion to biochar (450 °C), packaging, and distribution (up to 200 km). The analysis identified key environmental hotspots, with significant impacts associated with polypropylene packaging and transport logistics, despite the assumption of clean energy use for pyrolysis. These results demonstrate how LCA can guide process improvements, from exploring packaging alternatives to optimizing supply chains and increasing the use of renewable energy sources. Beyond serving as an environmental diagnostic, this work positions LCA as a scalable decision-support tool for resource-constrained agro-industrial contexts. It offers valuable support for industrial symbiosis initiatives and value chain enhancement. The proposed methodology is adaptable to other agro-industrial residues, helping industries reduce waste, improve carbon sequestration through biochar application in agriculture and contribute to climate action targets. Overall, the study advances the development of circular economy strategies in agro-industrial systems.